scholarly journals BIODIVERSITY ASSESSMENT OF MICROORGANISMS ASSOCIATED WITH TWO MARINE SPONGES (Haliclona oculata AND Amphius huxleyi) COLLECTED AT THE LANG CO BAY OF VIETNAM

2018 ◽  
Vol 18 (3) ◽  
pp. 286-295
Author(s):  
Ton That Huu Dat ◽  
Pham Viet Cuong ◽  
Tran Thi Dung Dung ◽  
Vu Thi Thu Huyen ◽  
Nguyen Thi Kim Cuc
Keyword(s):  
Illumina Miseq ◽  
Taxonomic Diversity ◽  
Marine Sponges ◽  
Sponge Species ◽  
Rrna Gene ◽  
Sponge Tissue ◽  
Biodiversity Assessment ◽  
Haliclona Oculata ◽  
Reference Sequences ◽  
The 16S Rrna Gene

Sponges (Phylum Porifera) are ancient sedentary and filter-feeding animals which harbour very diverse and abundant associated microbial community in their tissues with density up to 40–50% of sponge tissue volume. In this study, the diversity of associated microorganisms with two marine sponges Haliclona oculata and Amphius huxleyi collected at the Lang Co bay of Vietnam was assessed by analysis of hypervariable V3 and V4 regions of the 16S rRNA gene using Illumina MiSeq system. The taxonomic diversity of sponge-associated microorganisms was classified to different taxonomic levels (kingdom, phylum, class, order, family, and genus). Based on Bayesian classification method and reference sequences derived from Greengenes database, the associated microorganisms in studied sponges were assigned to 17 phyla (H. oculata) and 13 phyla (A. huxleyi). Many microbial taxa were detected in two sponge species, however, they were distinctive by the abundance. Proteobacteria was the most dominant phylum in both sponge species, and all of 4 classes Epsilonproteobacteria, Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria were found in H. oculata and A. huxleyi.

scholarly journals Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor

2020 ◽  
Vol 66 (9) ◽  
pp. 495-504
Author(s):  
Yan Zheng ◽  
Xiaolong Hu ◽  
Zhongjun Jia ◽  
Paul L.E. Bodelier ◽  
Zhiying Guo ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Prokaryotic Community ◽  
16S Rrna Gene Analysis ◽  
Pit Mud ◽  
Niche Competition ◽  
Occurrence Patterns ◽  
The 16S Rrna Gene

It is widely believed that the quality and characteristics of Chinese strong-flavor liquor (CSFL) are closely related to the age of the pit mud; CSFL produced from older pit mud tastes better. This study aimed to investigate the alteration and interaction of prokaryotic communities across an age gradient in pit mud. Prokaryotic microbes in different-aged pit mud (1, 6, and 10 years old) were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. Analysis of the 16S rRNA gene indicated that the prokaryotic community was significantly altered with pit mud age. There was a significant increase in the genera Methanosarcina, Methanobacterium, and Aminobacterium with increased age of pit mud, while the genus Lactobacillus showed a significant decreasing trend. Network analysis demonstrated that both synergetic co-occurrence and niche competition were dominated by 68 prokaryotic genera. These genera formed 10 hubs of co-occurrence patterns, mainly under the phyla Firmicutes, Euryarchaeota, and Bacteroidetes, playing important roles on ecosystem stability of the pit mud. Environmental variables (pH, NH4+, available P, available K, and Ca2+) correlated significantly with prokaryotic community assembly. The interaction of prokaryotic communities in the pit mud ecosystem and the relationship among prokaryotic communities and environmental factors contribute to the higher quality of the pit mud in older fermentation pits.

scholarly journals Impact of a Moderately Hypocaloric Mediterranean Diet on the Gut Microbiota Composition of Italian Obese Patients

Nutrients ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2707 ◽  
Author(s):  
Silvia Pisanu ◽  
Vanessa Palmas ◽  
Veronica Madau ◽  
Emanuela Casula ◽  
Andrea Deledda ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Mediterranean Diet ◽  
Illumina Miseq ◽  
Nutritional Intervention ◽  
Rrna Gene ◽  
Obese Patients ◽  
Dietary Interventions ◽  
The Impact ◽  
The 16S Rrna Gene ◽  
Gut Microbiota Composition

Although it is known that the gut microbiota (GM) can be modulated by diet, the efficacy of specific dietary interventions in determining its composition and diversity in obese patients remains to be ascertained. The present work aims to evaluate the impact of a moderately hypocaloric Mediterranean diet on the GM of obese and overweight patients (OB). The GM of 23 OB patients (F/M = 20/3) was compared before (T0) and after 3 months (T3) of nutritional intervention (NI). Fecal samples were analyzed by Illumina MiSeq sequencing of the 16S rRNA gene. At baseline, GM characterization confirmed typical obesity-associated dysbiosis. After 3 months of NI, patients presented a statistically significant reduction in body weight and fat mass, along with changes in the relative abundance of many microbial patterns. In fact, an increase in the abundance of several Bacteroidetes taxa (i.e., Sphingobacteriaceae, Sphingobacterium, Bacteroides spp., Prevotella stercorea) and a depletion of many Firmicutes taxa (i.e., Lachnospiraceae members, Ruminococcaceae and Ruminococcus, Veillonellaceae, Catenibacterium, Megamonas) were observed. In addition, the phylum Proteobacteria showed an increased abundance, while the genus Sutterella, within the same phylum, decreased after the intervention. Metabolic pathways, predicted by bioinformatic analyses, showed a decrease in membrane transport and cell motility after NI. The present study extends our knowledge of the GM profiles in OB, highlighting the potential benefit of moderate caloric restriction in counteracting the gut dysbiosis.

scholarly journals Detection and molecular characterisation of Ehrlichia canis in naturally infected dogs in South West Nigeria

2018 ◽  
Vol 66 (1) ◽  
pp. 85-95 ◽  
Author(s):  
Olukayode Olugbenga Daramola ◽  
Michael Irewole Takeet ◽  
Ibironke Kofoworola Oyewusi ◽  
Mufutau Atanda Oyekunle ◽  
Adewale Oladele Talabi
Keyword(s):  
Ehrlichia Canis ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Rickettsial Disease ◽  
Blood Samples ◽  
Canine Ehrlichiosis ◽  
South West ◽  
Polymerase Chain ◽  
Reference Sequences ◽  
The 16S Rrna Gene

Canine ehrlichiosis is an important tick-borne rickettsial disease mainly caused by Ehrlichia canis. This study aimed to detect and characterise E. canis in dogs in Abeokuta, Nigeria by microscopy and nested PCR. Blood samples were collected from 205 dogs, thin smears were made, field-stained, and DNA was extracted from the blood samples. A partial region of the 16S rRNA gene was amplified by polymerase chain reaction (PCR) and sequenced unidirectionally. Ehrlichial morulae were detected in three dogs (1.5%). The PCR test revealed that 47 dogs (22.9%) were positive for E. canis. The lengths of the sequences obtained range from 374 bp to 376 bp with an average G-C content of 37% and 98–99% homology with the reference sequences in GenBank. The aligned autochthonous sequences were less polymorphic. The phylogenetic analysis separated sequences reported previously in Nigeria from the autochthonous sequences. The present work shows that the strain of E. canis detected in the study area is genetically different from those reported in the northern part of Nigeria and more closely related to sequences from Brazil and India.

scholarly journals Resolving microbial microdiversity with high accuracy full length 16S rRNA Illumina sequencing

2014 ◽  
Author(s):  
Catherine Burke ◽  
Aaron E Darling
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Single Molecule ◽  
Illumina Miseq ◽  
Full Length ◽  
Rrna Gene ◽  
Variable Regions ◽  
Phylogenetic Resolution ◽  
Miseq Platform ◽  
The 16S Rrna Gene

We describe a method for sequencing full-length 16S rRNA gene amplicons using the high throughput Illumina MiSeq platform. The resulting sequences have about 100-fold higher accuracy than standard Illumina reads and are chimera filtered using information from a single molecule dual tagging scheme that boosts the signal available for chimera detection. We demonstrate that the data provides fine scale phylogenetic resolution not available from Illumina amplicon methods targeting smaller variable regions of the 16S rRNA gene.

scholarly journals Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
César Ruiz ◽  
Marcela Villegas-Plazas ◽  
Olivier P Thomas ◽  
Howard Junca ◽  
Thierry Pérez
Keyword(s):  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Sponge Species ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
16S Amplicon Sequencing ◽  
Ecological Success ◽  
Specific Community ◽  
First Time ◽  
The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

scholarly journals Molecular Detection of Fungal Communities in the Hawaiian Marine Sponges Suberites zeteki and Mycale armata

2008 ◽  
Vol 74 (19) ◽  
pp. 6091-6101 ◽  
Author(s):  
Zheng Gao ◽  
Binglin Li ◽  
Chengchao Zheng ◽  
Guangyi Wang
Keyword(s):  
Molecular Analysis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Terrestrial Ecosystems ◽  
Fungal Species ◽  
Marine Sponges ◽  
Fungal Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Significant Group ◽  
Marine Habitats

ABSTRACT Symbiotic microbes play a variety of fundamental roles in the health and habitat ranges of their hosts. While prokaryotes in marine sponges have been broadly characterized, the diversity of sponge-inhabiting fungi has barely been explored using molecular approaches. Fungi are an important component of many marine and terrestrial ecosystems, and they may be an ecologically significant group in sponge-microbe interactions. This study tested the feasibility of using existing fungal primers for molecular analysis of sponge-associated fungal communities. None of the eight selected primer pairs yielded satisfactory results in fungal rRNA gene or internal transcribed spacer (ITS) clone library constructions. However, 3 of 10 denaturing gradient gel electrophoresis (DGGE) primer sets, which were designed to preferentially amplify fungal rRNA gene or ITS regions from terrestrial environmental samples, were successfully amplified from fungal targets in marine sponges. DGGE analysis indicated that fungal communities differ among different sponge species (Suberites zeteki and Mycale armata) and also vary between sponges and seawater. Sequence analysis of DGGE bands identified 23 and 21 fungal species from each of the two sponge species S. zeteki and M. armata, respectively. These species were representatives of 11 taxonomic orders and belonged to the phyla of Ascomycota (seven orders) and Basidiomycota (four orders). Five of these taxonomic orders (Malasseziales, Corticiales, Polyporales, Agaricales, and Dothideomycetes et Chaetothyriomcetes incertae sedis) have now been identified for the first time in marine sponges. Seven and six fungal species from S. zeteki and M. armata, respectively, are potentially new species because of their low sequence identity (≤98%) with their references in GenBank. Phylogenetic analysis indicated sponge-derived sequences were clustered into “marine fungus clades” with those from other marine habitats. This is the first report of molecular analysis of fungal communities in marine sponges, adding depth and dimension to our understanding of sponge-associated microbial communities.

scholarly journals Uterine Microbiota Progression from Calving until Establishment of Metritis in Dairy Cows

2015 ◽  
Vol 81 (18) ◽  
pp. 6324-6332 ◽  
Author(s):  
Soo Jin Jeon ◽  
Achilles Vieira-Neto ◽  
Mohanathas Gobikrushanth ◽  
Rodolfo Daetz ◽  
Rodolfo D. Mingoti ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Heat Map ◽  
Content Type ◽  
Illumina Miseq Platform ◽  
Uterine Health ◽  
Miseq Platform ◽  
The 16S Rrna Gene

ABSTRACTThe objective of this study was to evaluate the progression of the uterine microbiota from calving until establishment of metritis. Uterine swabs (n= 72) collected at 0, 2, and 6 ± 2 days postpartum (dpp) from 12 metritic and 12 healthy cows were used for metagenomic sequencing of the 16S rRNA gene on the Illumina MiSeq platform. A heat map showed that uterine microbiota was established at calving. The microbiota changed rapidly from 0 to 6 ± 2 dpp, with a decrease in the abundance ofProteobacteriaand an increase in the abundance ofBacteroidetesandFusobacteria, which were dominant in metritic cows. Uterine microbiota composition was shared; however, metritic and healthy cows could be discriminated using relative abundance of bacterial genera at 0, 2, and 6 ± 2 dpp.Bacteroideswas the main genus associated with metritis because it was the only genus that showed significantly greater abundance in cows with metritis. As the abundance ofBacteroidesorganisms increased, the uterine discharge score, a measure of uterine health, worsened.Fusobacteriumwas also an important genus associated with metritis becauseFusobacteriumabundance increased asBacteroidesabundance increased and the uterine discharge score worsened as the abundance increased. The correlation with uterine discharge score and the correlation withBacteroidesorFusobacteriumshowed that other bacteria, such asHelcoccocus,Filifactor, andPorphyromonas, were also associated with metritis. There were also bacteria associated with uterine health, such as “CandidatusBlochmannia,”Escherichia,Sneathia, andPedobacter.

Single aflatoxin B1 exposure induces changes in gut microbiota community in C57Bl/6 mice

2017 ◽  
Vol 10 (3) ◽  
pp. 249-254 ◽  
Author(s):  
A.T. Ishikawa ◽  
J.S. Weese ◽  
A.P.F.R.L. Bracarense ◽  
A.A. Alfieri ◽  
G.G. Oliveira ◽  
...  
Keyword(s):  
Body Weight ◽  
Microbial Community ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Single Oral Administration ◽  
Aflatoxin B ◽  
Gut Microbial Community ◽  
The Impact ◽  
Harmful Effects ◽  
The 16S Rrna Gene

The liver and the gastrointestinal tract are the earliest target for the harmful effects of aflatoxin B1 (AFB1). This study investigated the impact of a single oral administration of AFB1 (663 µg of AFB1/kg of body weight) on the gut microbial community of C57Bl/6 mice. Sequencing of the V4 region of the 16S rRNA gene was performed with an Illumina MiSeq sequencer. AFB1 caused significant increases in the Lachnospiraceae family and decreases in Mucispirillum genus. In conclusion, a single oral dose of AFB1 changed the relative abundances of some taxa, but not the overall membership or structure of intestinal microbial communities in C57Bl/6 mice.

scholarly journals Nomenclature Errors in Public 16S rRNA Gene Reference Databases

2018 ◽  
Author(s):  
Kyle Lesack ◽  
Inanc Birol
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Standard Method ◽  
Marker Gene ◽  
Rrna Gene ◽  
High Quality ◽  
Quality Marker ◽  
Reference Databases ◽  
Reference Sequences ◽  
The 16S Rrna Gene

AbstractBackgroundTargeted gene surveys of the 16S rRNA gene have become a standard method for profiling the membership and biodiversity of microbial communities. These studies rely upon specialized databases that provide reference sequences and their corresponding taxonomic classifications, but few independent evaluations of the nomenclature used in the taxonomic classifications have been performed.ResultsNomenclature data collected from the List of Prokaryotic names with Standing in Nomenclature, Prokaryotic Nomenclature Up-to-Date, and CyanoDB databases were used to validate the nomenclature contained in the taxonomic classifications in the Greengenes, RDP, and SILVA 16S rRNA gene reference databases. Between 82% and 97% of the genus annotations assigned to 16S rRNA gene reference sequences were deemed valid in the reference databases. Between 18% and 97% of the species annotations in Greengenes and SILVA were deemed valid. Misannotations included the use of metadata in place of taxonomic classifications, non-adherence to the binomial nomenclature, and sequences classified as eukaryote organelles or taxa.ConclusionsThe misannotations identified in public 16S rRNA gene databases call into question the reliability of research made using these resources. As targeted gene surveys depend on high quality marker gene databases, imed nomenclature accuracy will be necessary.

scholarly journals Screening and characterization of sponge-associated bacteria from Seribu Island, Indonesia producing cellulase and laccase enzymes

2020 ◽  
Vol 21 (3) ◽  
Author(s):  
WENANG MAHARSIWI ◽  
RIKA INDRI ASTUTI ◽  
ANJA MERYANDINI ◽  
Aris Tri Wahyudi
Keyword(s):  
Extreme Environment ◽  
Marine Sponges ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Family Protein ◽  
Sponge Associated Bacteria ◽  
Pseudomonas Luteola ◽  
Modified Media ◽  
The 16S Rrna Gene

Abstract. Maharsiwi W, Astuti RI, Meryandini A, Wahyudi AT. 2020. Screening and characterization of sponge-associated bacteria from Seribu Island, Indonesia producing cellulase and laccase enzymes. Biodiversitas 21: 975-981. Exploration of new enzymes from an extreme environment is important to improve industrial efficiency. This study aimed to get sponge-associated bacteria from Seribu Island with the capability to produce cellulase and laccase. These enzyme activities were indicated by the clear zones on CMC medium for cellulase and the reddish-brown zone on Guaiacol medium for laccase. About 100 of sponge-associated bacteria have been isolated from 5 marine sponges used SWC and NA modified media. As screened, one isolate (AGN89) could produce both enzymes and 11 isolates could produce cellulase. Quantitative analysis was performed using the DNS method and obtained the activities of 4 best cellulolytic isolates ranged from 0.04-0.06 UmL-1 and 0.70-1.18 UmL-1 in enzyme and specific activities, respectively. Gene-based determination for the isolate producing laccase resulted in a ±1100 bp amplicon fragment which identified as multicopper oxidase family protein. Based on the 16S-rRNA gene, AGN89 and these 4 cellulolytic isolates were identified as Pseudomonas luteola strain NBRC 103146, Bacillus aerius strain 24k, Pseudomonas aeruginosa strain DSM 50071, Mycobacterium maritypicum strain DSM 20578, and Brachybacterium conglomeratum strain J 1015. This result suggests that the sponge-associated bacteria from Seribu Island could become new enzymes producer for further applications in industry.

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